The leading four cars were Commodores, underlining their dominance of the V8 Supercars competition.
The victory widens the gap between Whincup and the field - especially with nearest series challenger Mark Winterbottom finishing in tenth.
Heading to Bathurst next month, the reigning champion is now 273 points clear of teammate Craig Lowndes, with Winterbottom a further six points back.
After taking pole on Saturday, it became clear that only a driving error or strategic blunder could stop the Red Bull Racing pairing.
Even Whincup himself appeared to be taken aback by how simple winning the first endurance race of the season was.
"Our day was pretty straight forward which was perfect," he said.
"We all have the battle behind the scenes to try and make the car fast... I really enjoyed that this weekend and I feel like we got the balance pretty right."
Dumbrell built an impressive lead after starting well from the grid, handing over to Whincup after 85 of the 161 laps.
Holdsworth's crash on lap 133 set the stage for a 22-lap sprint finish to the 500 kilometre classic.
But Whincup was spared a challenge from Courtney with lapped cars denying car 22 a clear run after the re-start.
"That's the way it is," Courtney said.
"We wouldn't have had that chance otherwise because these lads had a few seconds on us."
In an already accomplished season, he and Dumbrell have also scrubbed two long-standing Sandown records.
Their back-to-back triumph is the first at Sandown since Murphy and Lowndes in 1996 and 1997, and the first pairing to win from pole in 18 years.
Whincup took great delight in winning from pole, telling his team via radio on the finish line "they said it couldn't be done".
After Lowndes in fourth, the best of the rest was emerging Ford driver Scott Pye and co-driver Ash Walsh with one of the best races of their V8 Supercars career.
V8 SUPERCARS CHAMPIONSHIP STANDINGS
1 Jamie Whincup (Holden) 2325
2 Craig Lowndes (Holden) - 273 behind
3 Mark Winterbottom (Ford) - 279
4 Shane van Gisbergen (Holden) -343
5 James Courtney (Holden) -361
6 Fabian Coulthard (Holden) -469
7 Chaz Mostert (Ford) -631
8 Scott McLaughlin (Volvo) -648
9 Garth Tander (Holden) -663